Research workbench

ARX1 pre-60S particle.

Analyse ARX1 pre-60S particle. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4V7F
Type: protein + RNA
Length: 12,068 residues
Chains: 48
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 25S ribosomal RNA; 5.8S ribosomal RNA; 5S ribosomal RNA; 60S ribosomal protein L1; 60S…
EC: 3.-.-.-
UniProt: P0CX43, P0CX45, P14126, P10664, P0C0W9, P05738, Q02326, P17076, P0CX53, P26784, Q12690, P0CX41, P36105, P02406, P05748, P26321, P0CX49, P0CX82, P0CX23, Q02753, P05740, P05749, P04456, P05743, P0C2H6, P0CX84, P05737, P14120, P0C2H8, P38061, P05744, P87262, P05745, P49166, P49167, P04650, P0CX25, Q03862, Q12522, P33201, Q02892, Q07915, P25382, P40693
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 47 distinct chains · 0% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	25S ribosomal RNA	rna	3394	—	—
2	5.8S ribosomal RNA	rna	158	—	—
3	5S ribosomal RNA	rna	121	—	—
A	60S ribosomal protein L1	protein	217	0% helix, 0% strand	P0CX43
B	60S ribosomal protein L2	protein	252	0% helix, 0% strand	P0CX45
C	60S ribosomal protein L3	protein	386	0% helix, 0% strand	P14126
D	60S ribosomal protein L4	protein	361	0% helix, 0% strand	P10664
E	60S ribosomal protein L11	protein	169	0% helix, 0% strand	P0C0W9
F	60S ribosomal protein L9	protein	191	0% helix, 0% strand	P05738
G	60S ribosomal protein L6	protein	175	0% helix, 0% strand	Q02326
H	60S ribosomal protein L8	protein	233	0% helix, 0% strand	P17076
I	60S ribosomal protein L12	protein	127	0% helix, 0% strand	P0CX53
J	60S ribosomal protein L16	protein	197	0% helix, 0% strand	P26784
K	60S ribosomal protein L13	protein	193	0% helix, 0% strand	Q12690
L	60S ribosomal protein L23	protein	136	0% helix, 0% strand	P0CX41
M	60S ribosomal protein L14	protein	136	0% helix, 0% strand	P36105
N	60S ribosomal protein L28	protein	148	0% helix, 0% strand	P02406
O	60S ribosomal protein L15	protein	203	0% helix, 0% strand	P05748
P	60S ribosomal protein L5	protein	269	0% helix, 0% strand	P26321
Q	60S ribosomal protein L18	protein	185	0% helix, 0% strand	P0CX49
R	60S ribosomal protein L19	protein	188	0% helix, 0% strand	P0CX82
S	60S ribosomal protein L20	protein	172	0% helix, 0% strand	P0CX23
T	60S ribosomal protein L21	protein	159	0% helix, 0% strand	Q02753
U	60S ribosomal protein L17	protein	183	0% helix, 0% strand	P05740
V	60S ribosomal protein L22	protein	100	0% helix, 0% strand	P05749
W	60S ribosomal protein L25	protein	121	0% helix, 0% strand	P04456
X	60S ribosomal protein L26	protein	126	0% helix, 0% strand	P05743
Y	60S ribosomal protein L27	protein	135	0% helix, 0% strand	P0C2H6
Z	60S ribosomal protein L35	protein	119	0% helix, 0% strand	P0CX84
a	60S ribosomal protein L7	protein	222	0% helix, 0% strand	P05737
b	60S ribosomal protein L30	protein	97	0% helix, 0% strand	P14120
c	60S ribosomal protein L31	protein	109	0% helix, 0% strand	P0C2H8
d	60S ribosomal protein L32	protein	127	0% helix, 0% strand	P38061
e	60S ribosomal protein L33	protein	106	0% helix, 0% strand	P05744
f	60S ribosomal protein L34	protein	112	0% helix, 0% strand	P87262
g	60S ribosomal protein L36	protein	99	0% helix, 0% strand	P05745
h	60S ribosomal protein L37	protein	87	0% helix, 0% strand	P49166
i	60S ribosomal protein L38	protein	77	0% helix, 0% strand	P49167
j	60S ribosomal protein L39	protein	50	0% helix, 0% strand	P04650
k	60S ribosomal protein L43	protein	91	0% helix, 0% strand	P0CX25
l	Metalloprotease ARX1 (EC 3.-.-.-)	protein	380	0% helix, 0% strand	Q03862
m	Eukaryotic translation initiation factor 6	protein	224	0% helix, 0% strand	Q12522
n	MRNA turnover protein 4	protein	236	0% helix, 0% strand	P33201
o	Nucleolar GTP-binding protein 1	protein	347	0% helix, 0% strand	Q02892
p	Ribosome biogenesis protein RLP24	protein	63	0% helix, 0% strand	Q07915
q	Ribosome assembly protein 4	protein	443	0% helix, 0% strand	P25382
r, s	Ribosome biogenesis protein RLP7	protein	322	0% helix, 0% strand	P40693

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	988	0.82	0.83	217	empty
2	1176	0.74	0.77	174	empty
3	898	0.74	0.78	129	empty
4	873	0.73	0.77	101	empty
5	374	0.72	0.84	68	empty

Interfaces

107 interfaces between chains.

r–s · 4958 Å² buried · 0 hydrogen bonds · protein-protein
1–C · 2581 Å² buried · 7 hydrogen bonds · protein-nucleic
1–D · 1708 Å² buried · 1 hydrogen bond · protein-nucleic
1–B · 1631 Å² buried · 2 hydrogen bonds · protein-nucleic
1–O · 1609 Å² buried · 1 hydrogen bond · protein-nucleic

Compared structures

4V7F · Arx1 pre-60S particle. · the same entry in another collection · chain E against E, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P0CX43
Every structure of UniProt P0CX45
Every structure of UniProt P14126
Every structure of UniProt P10664
Every structure of UniProt P0C0W9
Every structure of UniProt P05738
Every structure of UniProt Q02326
Every structure of UniProt P17076
Every structure of UniProt P0CX53
Every structure of UniProt P26784
Every structure of UniProt Q12690
Every structure of UniProt P0CX41
Every structure of UniProt P36105
Every structure of UniProt P02406
Every structure of UniProt P05748
Every structure of UniProt P26321
Every structure of UniProt P0CX49
Every structure of UniProt P0CX82
Every structure of UniProt P0CX23
Every structure of UniProt Q02753
Every structure of UniProt P05740
Every structure of UniProt P05749
Every structure of UniProt P04456
Every structure of UniProt P05743
Every structure of UniProt P0C2H6
Every structure of UniProt P0CX84
Every structure of UniProt P05737
Every structure of UniProt P14120
Every structure of UniProt P0C2H8
Every structure of UniProt P38061
Every structure of UniProt P05744
Every structure of UniProt P87262
Every structure of UniProt P05745
Every structure of UniProt P49166
Every structure of UniProt P49167
Every structure of UniProt P04650
Every structure of UniProt P0CX25
Every structure of UniProt Q03862
Every structure of UniProt Q12522
Every structure of UniProt P33201
Every structure of UniProt Q02892
Every structure of UniProt Q07915
Every structure of UniProt P25382
Every structure of UniProt P40693
Elsewhere: RCSB PDB 4V7F · PDBe 4V7F · UniProt P0CX43 · UniProt P0CX45 · UniProt P14126 · UniProt P10664 · UniProt P0C0W9 · UniProt P05738 · UniProt Q02326 · UniProt P17076 · UniProt P0CX53 · UniProt P26784 · UniProt Q12690 · UniProt P0CX41 · UniProt P36105 · UniProt P02406 · UniProt P05748 · UniProt P26321 · UniProt P0CX49 · UniProt P0CX82 · UniProt P0CX23 · UniProt Q02753 · UniProt P05740 · UniProt P05749 · UniProt P04456 · UniProt P05743 · UniProt P0C2H6 · UniProt P0CX84 · UniProt P05737 · UniProt P14120 · UniProt P0C2H8 · UniProt P38061 · UniProt P05744 · UniProt P87262 · UniProt P05745 · UniProt P49166 · UniProt P49167 · UniProt P04650 · UniProt P0CX25 · UniProt Q03862 · UniProt Q12522 · UniProt P33201 · UniProt Q02892 · UniProt Q07915 · UniProt P25382 · UniProt P40693

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